I'd like to see the ability to designate a part type as skeleton. This would be something that is automatically excluded from BOM calculation and mass.
Also, this would allow us to put in a reference control mechanism, to only allow external references to be created to the designated skeleton parts, making sure that modules and parts would become fully interchangable with only references to the skeleton.
Pro/E has had this for years and it's the basis for the Platform design and modularization modelling.
Solidworks